Abstract
Despite its economic, cultural and historical importance, few studies have investigated the evolutionary history of the domesticated apple (Malus domestica) as well as those of its wild relatives. Using new population genetic approaches (approximate Bayesian computation) with microsatellites and nuclear sequences, this thesis aimed to unravel, at different evolutionary scales (phylogeography, speciation, domestication), the natural and artificial diversification processes at play in the Malus genus. Research focused on the four wild apple species distributed across Eurasia [Malus orientalis (Caucasus), Malus sieversii (Central Asia), Malus sylvestris (Europe) and Malus baccata (Siberia)] and on the single domesticated apple species in the genus, Malus domestica. The thesis was divided into four parts: (1) domestication history of the cultivated apple, from its origin in Central Asia to Europe, (2) post-glacial recolonization history of the European crabapple (M. sylvestris), (3) the history of speciation among the five Malus species, (4) crop-to-wild gene flow and dispersal capacities of the closest wild relative species (M. sylvestris, M. sieversii and M. orientalis). By investigating artificial diversification, we found evidence of unique processes of domestication in this fruit tree, with no bottleneck and with extensive post-domestication introgressions by a wild species (M. sylvestris) other than the ancestral progenitor (M. sieversii). Natural diversification patterns (phylogeography, speciation and population structure) revealed large effective population sizes, high dispersal capacities and weak spatial genetic structures. This thesis also revealed high levels of interspecific hybridizations, and a particularly high level of crop-to-wild gene flow in Europe and Central Asia. This study extended our knowledge of population structures for the wild species that contributed to the cultivated apple genome, as well as the extent of hybridization rates. This work is essential for the conservation of wild apple populations, the maintenance of the integrity of wild species facing fragmentation and future breeding programmes concerning the domesticated apple.
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